On 7/09/2011 4:14 PM, aiswarya pawar wrote:
Hi Gromacs users,
Am running a MD simulation over a protein complex and before adding
the ions. we run a grompp option then we get result as model net
charge as some integer ie if +2.00. so we got to add 2 CL ions. But
when i ran my protein for grompp it didnt give me any net charge so am
not able to add any ions. is this correct??
There is no need to neutralize something that is already neutral.
Whether it should be neutral is a function of your termini and side
chains, and only you can address that. Whether you might want
charge-balanced ions in your aqueous phase is also something for you to
consider.
Mark
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